14-64596597-C-T

Variant names:

• chr14-64596597-C-T
• rs10134770
• ENST00000554454.1:n.-61G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554454.1(ENSG00000259076):​n.-61G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,198 control chromosomes in the GnomAD database, including 3,179 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (3179 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000259076 ENST00000554454.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 4 publications found

Genes affected

ENSG00000259076 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259076	ENST00000554454.1	n.-61G>A		upstream_gene_variant		5
ENSG00000259076	ENST00000556634.1	n.-84G>A		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28588 AN: 152080 Hom.: 3181 Cov.: 33

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.197

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.188 AC: 28585 AN: 152198 Hom.: 3179 Cov.: 33 AF XY: 0.188 AC XY: 13993 AN XY: 74410

African (AFR) AF: 0.0782 AC: 3248 AN: 41548

American (AMR) AF: 0.146 AC: 2232 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1110 AN: 5176

South Asian (SAS) AF: 0.200 AC: 967 AN: 4826

European-Finnish (FIN) AF: 0.262 AC: 2772 AN: 10576

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16827 AN: 67988

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.224 Hom.: 2155

Bravo AF: 0.174

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10134770; hg19: chr14-65063315;